He is reunited with Nigel Adkins, who also managed him at Glanford Park before leaving to take charge at St Mary's in September. The fee is undisclosed.
Doncaster-born Forte moved to the Iron in the summer of 2007, joining from Sheffield United as part of the deal that saw Billy Sharp return to his hometown club.
He was largely a bit-part player for the Iron until this season, when the departures of Gary Hooper and Paul Hayes saw him become first-choice. Despite being a regular starter, he managed only four goals.
"We've found that he's got pace, power, and he's got stronger and stronger," said Adkins, speaking to Southampton's official website.
"He's had a bit part to play [at Scunthorpe], but he can play on the left or right wing or as a centre forward.
"He's experienced in the Championship now. He's had a good couple of years and is a player who is getting better and better, and still only young.
"We're looking at the culture here and I know what his capabilities are. I know at times that he can be a little inconsistent as all young players can be, but I believe that bringing him into the environment that we've got down here he can only get better and better. He's going to enhance the group of players we've got."